Answers
The break-point problem: Have you debugged into assembler? You might have accidentally set a break-point on some assembler instruction. Look into the break-point list (Debug->Windows->Breakpoints; it's Alt+F9 for me) to see which breakpoints are set for the solution. Of course, source and binary not matching might also cause this. Alternatively the following might help, too.
Re the startup project: Visual Studio saves all user-specific data regarding a solution in a *.suo file which it puts right beside the *.sln file. This might have gotten corrupted (although I've never seen this). Try to delete it and see whether this helps. On a second thought, both problems might be caused by someone having checked in the *.suo file. Have you checked this?
Ctrl+Shift+F9 to 'Delete All Breakpoints' does not work.
Delete everything in your project which is not your source code: "obj" and "bin" sub-directories, all *.user and *.suo also from the hidden ".vs" directory.